Large-scale biophysical parameter estimation in single neurons via constrained linear regression. - Misha B. Ahrens; Quentin J. M. Huys; Liam Paninski (NIPS, 2005)

Inferring Elapsed Time from Stochastic Neural Processes. - Misha B. Ahrens; Maneesh Sahani (NIPS, 2007)

Multi-scale approaches for high-speed imaging and analysis of large neural populations. - Johannes Friedrich; Weijian Yang; Daniel Soudry; Yu Mu; Misha B. Ahrens; Rafael Yuste; Darcy S. Peterka; Liam Paninski (PLoS Comput. Biol., 2017)

Deformable Registration of Whole Brain Zebrafish Microscopy Using an Implementation of the Flash Algorithm Within Ants. - Greg M. Fleishman; Miaomiao Zhang; Nicholas J. Tustison; Isabel Espinosa-Medina; Yu Mu; Khaled Khairy; Misha B. Ahrens (ISBI, 2019)

Programmable 3D snapshot microscopy with Fourier convolutional networks. - Diptodip Deb; Zhenfei Jiao; Alex B. Chen; Misha B. Ahrens; Kaspar Podgorski; Srinivas C. Turaga (CoRR, 2021)

FourierNets enable the design of highly non-local optical encoders for computational imaging. - Diptodip Deb; Zhenfei Jiao; Ruth R. Sims; Alex B. Chen; Michael Broxton; Misha B. Ahrens; Kaspar Podgorski; Srinivas C. Turaga (NeurIPS, 2022)

BILCO: An Efficient Algorithm for Joint Alignment of Time Series. - Xuelong Mi; Mengfan Wang; Alex Bo-Yuan Chen; Jing-Xuan Lim; Yizhi Wang; Misha B. Ahrens; Guoqiang Yu (NeurIPS, 2022)

Dimensionality reduction of calcium-imaged neuronal population activity. - Tze Hui Koh; William E. Bishop; Takashi Kawashima; Brian B. Jeon; Ranjani Srinivasan; Yu Mu; Ziqiang Wei; Sandra J. Kuhlman; Misha B. Ahrens; Steven M. Chase; Byron M. Yu (Nat. Comput. Sci., 2023)

ZAPBench: A Benchmark for Whole-Brain Activity Prediction in Zebrafish. - Jan-Matthis Lueckmann; Alexander Immer; Alex Bo-Yuan Chen; Peter H. Li; Mariela D. Petkova; Nirmala A. Iyer; Luuk Willem Hesselink; Aparna Dev; Gudrun Ihrke; Woohyun Park; Alyson Petruncio; Aubrey Weigel; et al. (ICLR, 2025)

Forecasting Whole-Brain Neuronal Activity from Volumetric Video. - Alexander Immer; Jan-Matthis Lueckmann; Alex Bo-Yuan Chen; Peter H. Li; Mariela D. Petkova; Nirmala A. Iyer; Aparna Dev; Gudrun Ihrke; Woohyun Park; Alyson Petruncio; Aubrey Weigel; Wyatt Korff; et al. (CoRR, 2025)

POCO: Scalable Neural Forecasting through Population Conditioning. - Yu Duan; Hamza Tahir Chaudhry; Misha B. Ahrens; Christopher D. Harvey; Matthew G. Perich; Karl Deisseroth; Kanaka Rajan (CoRR, 2025)